lamindb 0.70.3__tar.gz → 0.70.4__tar.gz

{lamindb-0.70.3 → lamindb-0.70.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.70.3
+Version: 0.70.4
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,8 +9,8 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Dist: lnschema_core==0.65.1
-Requires-Dist: lamindb_setup==0.69.5
+Requires-Dist: lnschema_core==0.65.2
+Requires-Dist: lamindb_setup==0.70.0
 Requires-Dist: lamin_utils==0.13.2
 Requires-Dist: lamin_cli==0.12.3
 Requires-Dist: rapidfuzz
@@ -38,7 +38,7 @@ Requires-Dist: pytest-cov ; extra == "dev"
 Requires-Dist: nbproject_test>=0.5.1 ; extra == "dev"
 Requires-Dist: faker-biology ; extra == "dev"
 Requires-Dist: django-schema-graph ; extra == "erdiagram"
-Requires-Dist: readfcs>=1.1.7 ; extra == "fcs"
+Requires-Dist: readfcs>=1.1.8 ; extra == "fcs"
 Requires-Dist: fsspec[gs]==2023.12.2 ; extra == "gcp"
 Requires-Dist: nbproject==0.10.0 ; extra == "jupyter"
 Requires-Dist: nbstripout==0.6.1 ; extra == "jupyter"

{lamindb-0.70.3 → lamindb-0.70.4}/docs/changelog.md

@@ -14,6 +14,13 @@ When upgrading your LaminDB installation to a new `minor` version in `major.mino
 
 ## 0.70
 
+### 0.70.4 {small}`2024-04-24`
+
+- ✨ Allow passing path to `.from_anndata` [PR](https://github.com/laminlabs/lamindb/pull/1600) [@sunnyosun](https://github.com/sunnyosun)
+- 🚸 In `.setup.delete()`, check for data deletion & delete from hub [PR](https://github.com/laminlabs/lamindb/pull/1595) [@falexwolf](https://github.com/falexwolf)
+- ⚡️ Speed up `latest_version` [PR](https://github.com/laminlabs/lamindb/pull/1594) [@falexwolf](https://github.com/falexwolf)
+- 🚸 Better user feedback on folder-like artifacts [PR](https://github.com/laminlabs/lamindb/pull/1589) [@falexwolf](https://github.com/falexwolf)
+
 ### 0.70.3 {small}`2024-04-22`
 
 - 🚸 Update metadata like description upon re-running [PR](https://github.com/laminlabs/lamindb/pull/1588) [@falexwolf](https://github.com/falexwolf)

{lamindb-0.70.3 → lamindb-0.70.4}/docs/introduction.ipynb

@@ -898,21 +898,6 @@
     "\n",
     "LaminDB was influenced by many other projects, see {doc}`docs:influences`."
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "tags": [
-     "hide-cell"
-    ]
-   },
-   "outputs": [],
-   "source": [
-    "# clean up test instance\n",
-    "!lamin delete --force lamin-intro\n",
-    "!rm -r lamin-intro"
-   ]
   }
  ],
  "metadata": {

{lamindb-0.70.3 → lamindb-0.70.4}/docs/storage/vitessce.ipynb

@@ -20,11 +20,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import pytest\n",
-    "import lamindb as ln\n",
-    "\n",
-    "INSTANCE_NAME = \"test-vitessce\"\n",
-    "ln.setup.init(storage=f\"s3://lamindb-ci/{INSTANCE_NAME}\")"
+    "!lamin init --storage \"s3://lamindb-ci/test-vitessce\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import lamindb as ln"
    ]
   },
   {

{lamindb-0.70.3 → lamindb-0.70.4}/docs/tutorial.ipynb

@@ -54,6 +54,15 @@
     "You can now init a LaminDB instance with a directory `./lamin-tutorial` for storing data:"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!lamin init --storage ./lamin-tutorial  # or \"s3://my-bucket\" or \"gs://my-bucket\""
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -62,10 +71,6 @@
    "source": [
     "import lamindb as ln\n",
     "\n",
-    "ln.setup.init(storage=\"./lamin-tutorial\")  # or \"s3://my-bucket\" or \"gs://my-bucket\"\n",
-    "\n",
-    "# if new to LaminDB, set verbosity to hint level\n",
-    "\n",
     "ln.settings.verbosity = \"hint\""
    ]
   },
@@ -581,7 +586,7 @@
     "ln.Artifact.filter(\n",
     "    created_by=users.anonymous,\n",
     "    transform=transform,\n",
-    "    suffix=\".jpg\",\n",
+    "    suffix=\".csv\",\n",
     ").df().head()"
    ]
   },

{lamindb-0.70.3 → lamindb-0.70.4}/lamindb/__init__.py

@@ -40,7 +40,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.70.3"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.70.4"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 

{lamindb-0.70.3 → lamindb-0.70.4}/lamindb/_annotate.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Iterable, Optional
+from typing import TYPE_CHECKING, Iterable
 
 import anndata as ad
 import lamindb_setup as ln_setup
@@ -10,6 +10,7 @@ from lamindb_setup.core._docs import doc_args
 from lnschema_core import Artifact, Collection, Feature, Registry, Run, ULabel
 
 if TYPE_CHECKING:
+    from lamindb_setup.core.types import UPathStr
     from lnschema_core.types import FieldAttr
     from mudata import MuData
 
@@ -244,7 +245,7 @@ class DataFrameAnnotator:
         )
         return self._validated
 
-    def save_artifact(self, description: str, **kwargs) -> Artifact:
+    def save_artifact(self, description: str | None = None, **kwargs) -> Artifact:
         """Save the validated DataFrame and metadata.
 
         Args:
@@ -327,10 +328,10 @@ class DataFrameAnnotator:
 
 
 class AnnDataAnnotator(DataFrameAnnotator):
-    """Annotation flow for an ``AnnData`` object.
+    """Annotation flow for ``AnnData``.
 
     Args:
-        adata: The AnnData object to annotate.
+        data: The AnnData object or an AnnData-like path.
         var_index: The registry field for mapping the ``.var`` index.
         categoricals: A dictionary mapping ``.obs.columns`` to a registry field.
         using: A reference LaminDB instance.
@@ -349,14 +350,29 @@ class AnnDataAnnotator(DataFrameAnnotator):
 
     def __init__(
         self,
-        adata: ad.AnnData,
+        data: ad.AnnData | UPathStr,
         var_index: FieldAttr,
         categoricals: dict[str, FieldAttr] | None = None,
         using: str = "default",
         verbosity: str = "hint",
         organism: str | None = None,
     ) -> None:
-        self._adata = adata
+        from lamindb_setup.core import upath
+
+        from ._artifact import data_is_anndata
+
+        if not data_is_anndata(data):
+            raise ValueError(
+                "data has to be an AnnData object or a path to AnnData-like"
+            )
+        if isinstance(data, ad.AnnData):
+            self._adata = data
+        else:
+            from lamindb.core.storage._backed_access import backed_access
+
+            self._adata = backed_access(upath.create_path(data))
+
+        self._data = data
         self._var_field = var_index
         super().__init__(
             df=self._adata.obs,
@@ -443,7 +459,7 @@ class AnnDataAnnotator(DataFrameAnnotator):
         self._validated = validated_var and validated_obs
         return self._validated
 
-    def save_artifact(self, description: str, **kwargs) -> Artifact:
+    def save_artifact(self, description: str | None = None, **kwargs) -> Artifact:
         """Save the validated ``AnnData`` and metadata.
 
         Args:
@@ -457,7 +473,8 @@ class AnnDataAnnotator(DataFrameAnnotator):
             raise ValidationError("Please run `validate()` first!")
 
         self._artifact = save_artifact(
-            self._adata,
+            self._data,
+            adata=self._adata,
             description=description,
             columns_field=self.var_index,
             fields=self.categoricals,
@@ -697,7 +714,7 @@ class MuDataAnnotator:
         self._validated = validated_var and validated_obs
         return self._validated
 
-    def save_artifact(self, description: str, **kwargs) -> Artifact:
+    def save_artifact(self, description: str | None = None, **kwargs) -> Artifact:
         """Save the validated ``MuData`` and metadata.
 
         Args:
@@ -749,7 +766,7 @@ class Annotate:
     @doc_args(AnnDataAnnotator.__doc__)
     def from_anndata(
         cls,
-        adata: ad.AnnData,
+        data: ad.AnnData | UPathStr,
         var_index: FieldAttr,
         categoricals: dict[str, FieldAttr] | None = None,
         using: str = "default",
@@ -758,7 +775,7 @@ class Annotate:
     ) -> AnnDataAnnotator:
         """{}."""
         return AnnDataAnnotator(
-            adata=adata,
+            data=data,
             var_index=var_index,
             categoricals=categoricals,
             using=using,
@@ -920,10 +937,11 @@ def validate_categories_in_df(
 
 def save_artifact(
     data: pd.DataFrame | ad.AnnData | MuData,
-    description: str,
     fields: dict[str, FieldAttr] | dict[str, dict[str, FieldAttr]],
     columns_field: FieldAttr | dict[str, FieldAttr],
+    description: str | None = None,
     organism: str | None = None,
+    adata: ad.AnnData | None = None,
     **kwargs,
 ) -> Artifact:
     """Save all metadata with an Artifact.
@@ -934,15 +952,21 @@ def save_artifact(
         fields: A dictionary mapping obs_column to registry_field.
         columns_field: The registry field to validate variables index against.
         organism: The organism name.
+        adata: The AnnData object to save, must be provided if data is a path.
         kwargs: Additional keyword arguments to pass to the registry model.
 
     Returns:
         The saved Artifact.
     """
+    from ._artifact import data_is_anndata
+
     artifact = None
-    if isinstance(data, ad.AnnData):
+    if data_is_anndata(data):
+        assert adata is not None
         artifact = Artifact.from_anndata(data, description=description, **kwargs)
-        artifact.n_observations = data.n_obs
+        artifact.n_observations = adata.shape[0]
+        data = adata
+
     elif isinstance(data, pd.DataFrame):
         artifact = Artifact.from_df(data, description=description, **kwargs)
     else:

{lamindb-0.70.3 → lamindb-0.70.4}/lamindb/_artifact.py

@@ -463,7 +463,7 @@ def data_is_anndata(data: AnnData | UPathStr):
             if ".anndata" in data_path.suffixes:
                 return True
             # check only for local, expensive for cloud
-            if fsspec.utils.get_protocol(data_path) == "file":
+            if fsspec.utils.get_protocol(data_path.as_posix()) == "file":
                 return zarr_is_adata(data_path)
             else:
                 logger.warning("We do not check if cloud zarr is AnnData or not.")
@@ -597,6 +597,18 @@ def __init__(artifact: Artifact, *args, **kwargs):
     else:
         kwargs = kwargs_or_artifact
 
+    # in case we have a new version of a folder with a different hash, print a
+    # warning that the old version can't be recovered
+    if (
+        is_new_version_of is not None
+        and is_new_version_of.n_objects is not None
+        and is_new_version_of.n_objects > 1
+    ):
+        logger.warning(
+            f"artifact version {version} will _update_ the state of folder {is_new_version_of.path} - "
+            "to _retain_ the old state by duplicating the entire folder, do _not_ pass `is_new_version_of`"
+        )
+
     kwargs["uid"] = provisional_uid
     kwargs["version"] = version
     kwargs["description"] = description
@@ -652,7 +664,7 @@ def from_df(
 @doc_args(Artifact.from_anndata.__doc__)
 def from_anndata(
     cls,
-    adata: AnnData,
+    adata: AnnData | UPathStr,
     key: str | None = None,
     description: str | None = None,
     run: Run | None = None,
@@ -661,6 +673,8 @@ def from_anndata(
     **kwargs,
 ) -> Artifact:
     """{}."""
+    if not data_is_anndata(adata):
+        raise ValueError("data has to be an AnnData object or a path to AnnData-like")
     artifact = Artifact(
         data=adata,
         key=key,
@@ -916,7 +930,7 @@ def delete(
 ) -> None:
     # by default, we only move artifacts into the trash (visibility = -1)
     trash_visibility = VisibilityChoice.trash.value
-    if self.visibility > trash_visibility and permanent is not True:
+    if self.visibility > trash_visibility and not permanent:
         if storage is not None:
             logger.warning("moving artifact to trash, storage arg is ignored")
         # move to trash
@@ -935,41 +949,44 @@ def delete(
         )
         delete_record = response == "y"
     else:
-        # this second option doesn't feel very intuitive
-        delete_record = permanent
+        assert permanent
+        delete_record = True
 
-    if delete_record is True:
+    if delete_record:
         # need to grab file path before deletion
         try:
-            filepath = filepath_from_artifact(self, using_key)
+            path = filepath_from_artifact(self, using_key)
         except OSError:
             # we can still delete the record
+            logger.warning("Could not get path")
             storage = False
         # only delete in storage if DB delete is successful
         # DB delete might error because of a foreign key constraint violated etc.
         self._delete_skip_storage()
         if self.key is None or self.key_is_virtual:
-            # always delete in storage if the key is virtual
-            delete_in_storage = True
-            if storage is not None:
-                logger.warning("storage arg is ignored if storage key is non-semantic")
+            # do not ask for confirmation also if storage is None
+            delete_in_storage = storage is None or storage
         else:
             # for artifacts with non-virtual semantic storage keys (key is not None)
             # ask for extra-confirmation
             if storage is None:
                 response = input(
-                    f"Are you sure to want to delete {filepath}? (y/n)  You can't undo"
+                    f"Are you sure to want to delete {path}? (y/n)  You can't undo"
                     " this action."
                 )
                 delete_in_storage = response == "y"
             else:
                 delete_in_storage = storage
+        if not delete_in_storage:
+            logger.warning(
+                f"you will retain a dangling store here: {path}, not referenced via an artifact"
+            )
         # we don't yet have logic to bring back the deleted metadata record
         # in case storage deletion fails - this is important for ACID down the road
-        if delete_in_storage is True:
-            delete_msg = delete_storage(filepath)
+        if delete_in_storage:
+            delete_msg = delete_storage(path)
             if delete_msg != "did-not-delete":
-                logger.success(f"deleted {colors.yellow(f'{filepath}')}")
+                logger.success(f"deleted {colors.yellow(f'{path}')}")
 
 
 def _delete_skip_storage(artifact, *args, **kwargs) -> None:

{lamindb-0.70.3 → lamindb-0.70.4}/lamindb/_query_set.py

@@ -286,9 +286,11 @@ class QuerySet(models.QuerySet, CanValidate, IsTree):
 
 
 def filter_query_set_by_latest_version(ordered_query_set: QuerySet) -> RecordsList:
-    if len(ordered_query_set) == 0:
+    # evaluating length can be very costly, hence, the try-except block
+    try:
+        first_record = ordered_query_set[0]
+    except IndexError:
         return ordered_query_set
-    first_record = ordered_query_set[0]
     records_in_view = {}
     records_in_view[first_record.stem_uid] = first_record
     for record in ordered_query_set:

{lamindb-0.70.3 → lamindb-0.70.4}/lamindb/_save.py

@@ -171,7 +171,7 @@ def copy_or_move_to_cache(artifact: Artifact, storage_path: UPath):
     cache_dir = settings._storage_settings.cache_dir
 
     # just delete from the cache dir if a local instance
-    if not lamindb_setup.settings.storage.is_cloud:
+    if not lamindb_setup.settings.storage.type_is_cloud:
         if cache_dir in local_path.parents:
             if is_dir:
                 shutil.rmtree(local_path)

{lamindb-0.70.3 → lamindb-0.70.4}/lamindb/core/_data.py

@@ -357,7 +357,12 @@ def _track_run_input(
     is_run_input: bool | None = None,
     run: Run | None = None,
 ):
-    if run is None:
+    # this is an internal hack right now for project-flow, but we can allow this
+    # for the user in the future
+    if isinstance(is_run_input, Run):
+        run = is_run_input
+        is_run_input = True
+    elif run is None:
         run = run_context.run
     # consider that data is an iterable of Data
     data_iter: Iterable[Data] = [data] if isinstance(data, Data) else data

{lamindb-0.70.3 → lamindb-0.70.4}/lamindb/integrations/_vitessce.py

@@ -39,15 +39,15 @@ def save_vitessce_config(vitessce_config: VitessceConfig, description: str) -> A
             if "url" not in file:
                 raise ValueError("Each file must have a 'url' key.")
             filename = file["url"].split("/")[-1]
-            assert filename.endswith((".anndata.zarr", ".spatialdata.zarr", ".zarr"))
-            filestem = (
-                filename.replace(".anndata.zarr", "")
-                .replace(".spatialdata.zarr", "")
-                .replace(".zarr", "")
+            assert filename.endswith((".anndata.zarr", ".spatialdata.zarr"))
+            filestem = filename.replace(".anndata.zarr", "").replace(
+                ".spatialdata.zarr", ""
             )
             artifact = Artifact.filter(uid__startswith=filestem).one_or_none()
             if artifact is None:
-                logger.warning(f"could not find dataset in lamindb: {dataset}")
+                logger.warning(
+                    f"could not find dataset '{filestem}' in lamindb: {dataset}"
+                )
             else:
                 input_artifacts.append(artifact)
     # link inputs

{lamindb-0.70.3 → lamindb-0.70.4}/noxfile.py

@@ -46,8 +46,9 @@ def lint(session: nox.Session) -> None:
     ["unit", "tutorial", "guide", "biology", "faq", "storage", "docs", "cli"],
 )
 def install(session, group):
-    # run with pypi install on main
-    if os.getenv("GITHUB_EVENT_NAME") != "push":
+    # on the release branch, do not use submodules but run with pypi install
+    # only exception is the docs group
+    if os.getenv("GITHUB_EVENT_NAME") != "push" or group == "docs":
         # run with submodule install on a PR
         submodules = " ".join(
             [
@@ -160,6 +161,7 @@ def docs(session):
                 section = (
                     "```\n\n" + "#" * len(names) + " " + " ".join(("lamin", *names[1:]))
                 )
+            help_string = help_string.replace("Usage: main", "Usage: lamin")
             page += f"{section}\n\n```\n{help_string}```\n\n"
 
         Path("./docs/cli.md").write_text(page)

{lamindb-0.70.3 → lamindb-0.70.4}/pyproject.toml

@@ -16,8 +16,8 @@ classifiers = [
 ]
 dependencies = [
     # Lamin PINNED packages
-    "lnschema_core==0.65.1",
-    "lamindb_setup==0.69.5",
+    "lnschema_core==0.65.2",
+    "lamindb_setup==0.70.0",
     "lamin_utils==0.13.2",
     "lamin_cli==0.12.3",
     # others
@@ -58,7 +58,7 @@ zarr = [
     "zarr>=2.16.0",
 ]
 fcs = [
-    "readfcs>=1.1.7",
+    "readfcs>=1.1.8",
 ]
 erdiagram = [
     "django-schema-graph",

{lamindb-0.70.3 → lamindb-0.70.4}/sub/lamin-cli/tests/scripts/initialized.py

@@ -13,3 +13,5 @@ if __name__ == "__main__":
     ln.track(new_run=False)
 
     print("hello!")
+
+    ln.finish()

{lamindb-0.70.3 → lamindb-0.70.4}/sub/lamin-cli/tests/test_get.py

@@ -3,7 +3,7 @@ import subprocess
 
 
 def test_decompose_url():
-    url = "https://lamin.ai/laminlabs/arrayloader-benchmarks/core/transform/1GCKs8zLtkc85zKv"  # noqa
+    url = "https://lamin.ai/laminlabs/arrayloader-benchmarks/transform/1GCKs8zLtkc85zKv"  # noqa
     result = decompose_url(url)
     instance_slug, entity, uid = result
     assert instance_slug == "laminlabs/arrayloader-benchmarks"
@@ -14,7 +14,7 @@ def test_decompose_url():
 def test_get():
     result = subprocess.run(
         "lamin get"
-        " 'https://lamin.ai/laminlabs/arrayloader-benchmarks/core/transform/1GCKs8zLtkc85zKv'",  # noqa
+        " 'https://lamin.ai/laminlabs/arrayloader-benchmarks/transform/1GCKs8zLtkc85zKv'",  # noqa
         shell=True,
         capture_output=True,
     )

{lamindb-0.70.3 → lamindb-0.70.4}/sub/lamindb-setup/docs/changelog.md

@@ -3,6 +3,10 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+✨ Introduce `local_storage` mode for cloud instances | [728](https://github.com/laminlabs/lamindb-setup/pull/728) | [falexwolf](https://github.com/falexwolf) | 2024-04-23 | 0.70.0
+🚚 Make `.uuid` attributes private | [727](https://github.com/laminlabs/lamindb-setup/pull/727) | [falexwolf](https://github.com/falexwolf) | 2024-04-23 |
+🚚 Rename `is_cloud` to `type_is_cloud` | [726](https://github.com/laminlabs/lamindb-setup/pull/726) | [falexwolf](https://github.com/falexwolf) | 2024-04-23 |
+🚸 In `.delete()`, check for data deletion & delete from hub | [725](https://github.com/laminlabs/lamindb-setup/pull/725) | [falexwolf](https://github.com/falexwolf) | 2024-04-22 |
 ✨ Upload dirs inplace | [722](https://github.com/laminlabs/lamindb-setup/pull/722) | [Koncopd](https://github.com/Koncopd) | 2024-04-20 | 0.69.5
 ♻️ Do not always read from local cache | [720](https://github.com/laminlabs/lamindb-setup/pull/720) | [falexwolf](https://github.com/falexwolf) | 2024-04-19 | 0.69.4
 ♻️ Improve suffix handling | [718](https://github.com/laminlabs/lamindb-setup/pull/718) | [falexwolf](https://github.com/falexwolf) | 2024-04-19 | 0.69.3

lamindb-0.70.4/sub/lamindb-setup/docs/hub-cloud/01-init-local-instance.ipynb

@@ -0,0 +1,114 @@
+{
+ "cells": [
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {
+    "tags": []
+   },
+   "source": [
+    "# Init a local instance"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!lamin login testuser1"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import lamindb_setup as ln_setup"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ln_setup.init(storage=\"./mydata\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "hide-cell"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "from pathlib import Path\n",
+    "\n",
+    "assert ln_setup.settings.instance.storage.type_is_cloud == False\n",
+    "assert ln_setup.settings.instance.owner == ln_setup.settings.user.handle\n",
+    "assert ln_setup.settings.instance.name == \"mydata\"\n",
+    "assert ln_setup.settings.storage.root.as_posix() == Path(\"mydata\").resolve().as_posix()\n",
+    "storage_root = ln_setup.settings.storage.root\n",
+    "assert storage_root.exists()\n",
+    "assert ln_setup.settings.storage.id is not None\n",
+    "assert (\n",
+    "    ln_setup.settings.instance.db\n",
+    "    == f\"sqlite:///{Path('./mydata').resolve().as_posix()}/{ln_setup.settings.instance.id.hex}.lndb\"\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ln_setup.delete(\"mydata\", force=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from lamindb_setup.core._settings_store import instance_settings_file\n",
+    "\n",
+    "settings_file = instance_settings_file(\"mydata\", \"testuser1\")\n",
+    "assert not storage_root.exists()\n",
+    "assert settings_file.exists() == False"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.13"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "40d3a090f54c6569ab1632332b64b2c03c39dcf918b08424e98f38b5ae0af88f"
+   }
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}